L02 : Protein structure and function
L02 Protein structure and function Transcription and translation DNA acts as a template and is transcribed onto mRNA (AUCG) by RNA polymerase Protein structure Proteins are composed of several structures: Primary structure This includes the polypeptide chain Secondary structure This involves helices and pleated sheets Polypeptide chains often fold into a helices and b sheets, which are common folding patterns Tertiary structure This is the 3d shape of the protein which requires the lowest amount of energy Arrangement of amino acids Improper folding When proteins fold improperly, they can form aggregates Quaternary structure This involves more than one polypeptide chain Disulphide bonds Many proteins molecules are attached to the outside of the plasma membrane or attached to the ECM Function The disulphide bonds reinforce the most favoured conformation Protein diversity Proteins may be of several different types: The type of protein will suit its function Function Proteins have several functions including: All proteins will bind to other molecules in some way at their binding site Regulation of function Example: Regulation of gene expression Proteins are only synthesised when and where they are needed, including: Feedback inhibition The catalytic activity of enzymes are often regulated by other molecules Protein modification Proteins are modified in the endoplasmic reticulum Adding small molecules can add extra functions to proteins (e.g. Haemoglobin) Dynamic nature of proteins (protein activation) The structural arrangement (conformation) of a protein is dynamic Mechanism The shift in conformation change is required for function such as enzyme activation, substrate binding Example: CDK and cyclin Catalytic protein is cyclin dependent kinase (cdK) Secretory pathway This involves: Secretory vesicles If defective or not needed, they can be taken to lysosomes to be degraded Transport vesicles Soluble proteins are transported in the cell via a transport vesicle Molecules transported Constitutive secretion occurs this way Transport to ER, mitochondria, peroxisomes Transport into nucleus Application: Cystic fibrosis In cystic fibrosis, the CFTR protein is mutated #3 mRNA form a codon #This corresponds to an amino acid #The mRNA chain is translated on a ribosome into a protein #As there are 64 possible codes yet 20 amino acid, some of the code is redundant/regulatory #Primary #Secondary #Tertiary #Quaternary (only some proteins) #Amino acids are linked by peptide bonds #Various side chains are exposed #These have properties such as polarity/non-polarity, hydrophobic/philic , + or - charge #These are stabilised by Van der Waals, hydrogen bonds and electrostatic attraction #Alpha helices are stabilised by hydrogen bonds #This is known as the conformation (this may be changed by other molecules binding) #In enzymes, the active site is specific and complimentary to its substrate #Non-polar (hydrophobic) amino acids tend to be inside of the protein #Polar(hydrophilic) amino acids tend to be on the outside of the protein #This can damage cells and tissues (especially if infectious) #This is shown in Alzheimer's and Huntington's #The subunits may be homomers (same) or heretomers (different) #Therefore, to help stabilize them, the polypeptide chains are stabilized by covalent cross-linkages #The most common cross-link is the disulphide bond (S-S bond) #These forms as proteins are exported from cells #The formation is catalysed in the ER by an enzyme which links cysteine side chains together #They do not form in the cell cytosol #This is because there is a high concentration of reducing agents (this converts such bonds back to -SH groups) #Fibrous: Collagen #Globular: Secretory, can be enzymes, haemoglobin. Usually hydrophobic in, and hydrophilic on the outside. #Catalysis: Enzymes #Receptors: Binding ligands(an ion/small molecule/macromolecule which binds to protein) #Switching: Signalling pathways #Structural : Cytoskeletal element, gives cell shape, helps organelles move #Synthesis: Is it present or not? #Localisation : Is it where it needs to be? #Modification: Active/inactive? #Degradation : Is it needed anymore? #Cell differentiation and specialisation #Immune response #In response to signals from other cells #This is done through feedback inhibition #An enzyme acting early in the reaction pathway is inhibited by a later product #Therefore, this reduces the quantity of the later product #Disulphide bonds (reinforce conformation) and glycosylation occurs (adding sugar) #Further modification occurs in the golgi #The conformation can shift to suit the function #This requires phosphorylation (catalysed by protein kinase) #Dephosphorylation is done by protein phosphatase #The phosphate is attached to the protein chain #This inhibits or activates the protein #Therefore, it leads to a conformation change #This is only active when cyclin is present #This allows for a change in conformation #Secretory vesicles #Transport vesicles #Proteins may also be stored in secretory vesicles until an extracellular signal causes them to fuse with the cell membrane #This causes the proteins to be released #The proteins have a sorting signal to direct them to the correct site #They may be taken to organelles where they are required #They can be transported from one compartment to another via transport vesicles #Plasma membrane proteins are transported in this fashion #Proteins are taken to endosomes and lysosomes for degradation #Transport to these organelles from to cytosol is carried out by protein translocation #The molecule will unfold to get through the membrane #Proteins move in via the nuclear pores #The pores are selective gates which actively transport specific macromolecules #This is caused by the deletion of an amino acid #This causes the mutated protein to be incorrectly folded and retained in the ER (degraded, never reaches the membrane)